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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-09-10, 05:30 CEST based on data in:
        • /home/sararomi/nora/SA_polony/SA_polony50/qc
        • /home/sararomi/nora/SA_polony/SA_polony50/trim
        • /home/sararomi/nora/SA_polony/SA_polony50/assemblies
        • /home/sararomi/nora/SA_polony/SA_polony50/quast_results
        • /home/sararomi/nora/SA_polony/SA_polony50/amr

        General Statistics

        Showing 149/149 rows and 11/15 columns.
        Sample NameN50 (Kbp)Assembly Length (Mbp)% Duplication% > Q30Mb Q30 basesReads After FilteringGC content% PF% AdapterDupsGCAvg lenMedian lenFailedSeqs
        SRR27013147_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        462.7Mb
        1.9M
        41.2%
        97.6%
        3.3%
        33.2%
        41.0%
        245bp
        294bp
        9%
        1.0M
        SRR27013147_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        30.0%
        41.0%
        246bp
        294bp
        9%
        1.0M
        SRR27013147_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        182.2Kbp
        3.1Mbp
        SRR27013245_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        348.8Mb
        1.3M
        46.7%
        99.9%
        1.7%
        17.8%
        46.0%
        278bp
        301bp
        18%
        0.6M
        SRR27013245_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        15.7%
        46.0%
        278bp
        301bp
        18%
        0.6M
        SRR27013245_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        45.1Kbp
        8.4Mbp
        SRR27013246_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        100.0%
        273.8Mb
        1.0M
        41.2%
        99.9%
        1.2%
        25.0%
        41.0%
        279bp
        301bp
        9%
        0.5M
        SRR27013246_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        21.5%
        41.0%
        279bp
        301bp
        9%
        0.5M
        SRR27013246_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        106.6Kbp
        3.0Mbp
        SRR27013247_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        239.8Mb
        0.8M
        40.8%
        99.9%
        1.0%
        21.4%
        40.0%
        287bp
        301bp
        9%
        0.4M
        SRR27013247_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        18.0%
        40.0%
        287bp
        301bp
        9%
        0.4M
        SRR27013247_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        74.6Kbp
        3.1Mbp
        SRR27013248_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        326.0Mb
        1.2M
        41.5%
        99.9%
        1.7%
        28.0%
        41.0%
        270bp
        301bp
        9%
        0.6M
        SRR27013248_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        25.5%
        41.0%
        270bp
        301bp
        9%
        0.6M
        SRR27013248_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        32.7Kbp
        3.0Mbp
        SRR27013249_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        100.0%
        294.2Mb
        1.1M
        40.8%
        99.9%
        1.3%
        23.8%
        40.0%
        272bp
        301bp
        9%
        0.5M
        SRR27013249_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        21.0%
        40.0%
        273bp
        301bp
        9%
        0.5M
        SRR27013249_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        64.3Kbp
        3.0Mbp
        SRR27013250_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        379.4Mb
        1.4M
        40.9%
        99.9%
        1.3%
        28.1%
        40.0%
        273bp
        301bp
        9%
        0.7M
        SRR27013250_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        25.7%
        40.0%
        274bp
        301bp
        9%
        0.7M
        SRR27013250_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        75.0Kbp
        3.0Mbp
        SRR27013251_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        1.5%
        100.0%
        284.0Mb
        1.0M
        42.3%
        100.0%
        1.3%
        30.6%
        42.0%
        285bp
        301bp
        18%
        0.5M
        SRR27013251_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        27.4%
        42.0%
        286bp
        301bp
        18%
        0.5M
        SRR27013251_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        10.8Kbp
        5.3Mbp
        SRR27013252_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        306.3Mb
        1.1M
        41.5%
        99.9%
        1.2%
        28.2%
        41.0%
        273bp
        301bp
        9%
        0.6M
        SRR27013252_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        25.4%
        41.0%
        273bp
        301bp
        9%
        0.6M
        SRR27013253_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        100.0%
        289.1Mb
        1.0M
        40.5%
        99.9%
        1.0%
        22.6%
        40.0%
        286bp
        301bp
        9%
        0.5M
        SRR27013253_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        19.5%
        40.0%
        286bp
        301bp
        9%
        0.5M
        SRR27013253_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        72.4Kbp
        3.1Mbp
        SRR27013254_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        324.6Mb
        1.2M
        41.0%
        100.0%
        2.5%
        25.4%
        40.0%
        272bp
        301bp
        9%
        0.6M
        SRR27013254_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        22.8%
        41.0%
        273bp
        301bp
        9%
        0.6M
        SRR27013254_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        32.0Kbp
        3.0Mbp
        SRR27013255_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        278.3Mb
        1.1M
        41.1%
        99.9%
        7.9%
        23.5%
        40.0%
        245bp
        294bp
        9%
        0.6M
        SRR27013255_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        20.1%
        41.0%
        249bp
        301bp
        9%
        0.6M
        SRR27013255_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        91.3Kbp
        3.0Mbp
        SRR27013256_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        318.2Mb
        1.2M
        40.8%
        100.0%
        2.7%
        24.5%
        40.0%
        269bp
        301bp
        9%
        0.6M
        SRR27013256_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        22.0%
        40.0%
        270bp
        301bp
        9%
        0.6M
        SRR27013256_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        55.1Kbp
        3.1Mbp
        SRR27013257_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        286.8Mb
        1.0M
        40.7%
        100.0%
        2.2%
        21.8%
        40.0%
        282bp
        301bp
        9%
        0.5M
        SRR27013257_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        17.4%
        40.0%
        283bp
        301bp
        9%
        0.5M
        SRR27013257_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        33.1Kbp
        3.0Mbp
        SRR27013258_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        286.5Mb
        1.0M
        40.9%
        100.0%
        2.3%
        22.4%
        40.0%
        278bp
        301bp
        9%
        0.5M
        SRR27013258_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        18.8%
        40.0%
        278bp
        301bp
        9%
        0.5M
        SRR27013258_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        27.6Kbp
        3.0Mbp
        SRR27013259_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        287.9Mb
        1.0M
        40.5%
        100.0%
        2.5%
        21.3%
        40.0%
        283bp
        301bp
        9%
        0.5M
        SRR27013259_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        16.3%
        40.0%
        283bp
        301bp
        9%
        0.5M
        SRR27013259_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        24.4Kbp
        3.1Mbp
        SRR27013260_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        343.9Mb
        1.2M
        40.9%
        99.9%
        2.3%
        25.5%
        40.0%
        276bp
        301bp
        9%
        0.6M
        SRR27013260_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        21.1%
        41.0%
        277bp
        301bp
        9%
        0.6M
        SRR27013260_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        32.0Kbp
        3.0Mbp
        SRR27013261_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        313.0Mb
        1.3M
        41.3%
        99.9%
        2.9%
        26.8%
        41.0%
        246bp
        294bp
        9%
        0.6M
        SRR27013261_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        23.6%
        41.0%
        247bp
        301bp
        9%
        0.6M
        SRR27013261_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        98.0Kbp
        3.0Mbp
        SRR27013262_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        354.5Mb
        1.3M
        40.9%
        100.0%
        2.3%
        25.5%
        40.0%
        276bp
        301bp
        9%
        0.6M
        SRR27013262_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        21.4%
        40.0%
        276bp
        301bp
        9%
        0.6M
        SRR27013262_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        38.9Kbp
        3.1Mbp
        SRR27013263_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        100.0%
        338.7Mb
        1.4M
        41.2%
        99.9%
        3.0%
        27.2%
        41.0%
        251bp
        294bp
        9%
        0.7M
        SRR27013263_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        24.2%
        41.0%
        252bp
        301bp
        9%
        0.7M
        SRR27013263_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        87.5Kbp
        3.0Mbp
        SRR27013264_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        359.9Mb
        1.4M
        41.0%
        99.9%
        3.0%
        27.5%
        40.0%
        252bp
        301bp
        9%
        0.7M
        SRR27013264_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        22.5%
        41.0%
        253bp
        301bp
        9%
        0.7M
        SRR27013264_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        101.4Kbp
        3.0Mbp
        SRR27013265_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.5%
        100.0%
        512.8Mb
        2.2M
        41.3%
        97.7%
        3.6%
        35.3%
        41.0%
        239bp
        284bp
        9%
        1.1M
        SRR27013265_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        31.7%
        41.0%
        240bp
        284bp
        9%
        1.1M
        SRR27013265_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        119.8Kbp
        3.0Mbp
        SRR27013266_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        100.0%
        447.7Mb
        1.8M
        41.2%
        97.6%
        3.4%
        32.8%
        41.0%
        252bp
        301bp
        9%
        0.9M
        SRR27013266_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        28.2%
        41.0%
        253bp
        301bp
        9%
        0.9M
        SRR27013266_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        228.4Kbp
        3.0Mbp
        SRR27013267_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        406.2Mb
        1.7M
        41.5%
        99.9%
        3.0%
        31.1%
        41.0%
        245bp
        284bp
        9%
        0.8M
        SRR27013267_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        29.1%
        41.0%
        245bp
        284bp
        9%
        0.8M
        SRR27013267_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        57.3Kbp
        3.0Mbp
        SRR27013268_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.8%
        87.7%
        491.0Mb
        2.6M
        40.8%
        96.5%
        3.8%
        36.2%
        40.0%
        217bp
        244bp
        18%
        1.3M
        SRR27013268_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        33.1%
        40.0%
        218bp
        244bp
        27%
        1.3M
        SRR27013268_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        295.2Kbp
        3.0Mbp
        SRR27013269_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        85.3%
        316.2Mb
        1.5M
        41.2%
        95.7%
        3.7%
        29.4%
        41.0%
        249bp
        294bp
        18%
        0.8M
        SRR27013269_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        26.0%
        41.0%
        250bp
        301bp
        27%
        0.8M
        SRR27013269_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        93.3Kbp
        3.0Mbp
        SRR27013270_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.1%
        100.0%
        233.0Mb
        0.8M
        40.5%
        99.9%
        5.7%
        18.5%
        40.0%
        281bp
        301bp
        9%
        0.4M
        SRR27013270_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        15.4%
        40.0%
        283bp
        301bp
        9%
        0.4M
        SRR27013270_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        38.0Kbp
        3.0Mbp
        SRR27013271_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        100.0%
        370.4Mb
        1.5M
        41.2%
        97.7%
        4.2%
        29.2%
        41.0%
        242bp
        294bp
        9%
        0.8M
        SRR27013271_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        25.3%
        41.0%
        244bp
        294bp
        9%
        0.8M
        SRR27013271_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        75.8Kbp
        3.0Mbp
        SRR27013272_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        320.6Mb
        1.3M
        41.2%
        99.8%
        3.6%
        26.1%
        41.0%
        242bp
        294bp
        9%
        0.7M
        SRR27013272_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        23.4%
        41.0%
        243bp
        294bp
        9%
        0.7M
        SRR27013272_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        98.7Kbp
        3.1Mbp
        SRR27013273_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        100.0%
        474.3Mb
        1.8M
        41.3%
        97.5%
        3.3%
        34.9%
        41.0%
        259bp
        301bp
        9%
        0.9M
        SRR27013273_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        30.6%
        41.0%
        260bp
        301bp
        9%
        0.9M
        SRR27013273_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        110.6Kbp
        3.0Mbp
        SRR27013274_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.5%
        100.0%
        451.1Mb
        1.9M
        41.4%
        99.8%
        4.8%
        32.3%
        41.0%
        233bp
        274bp
        9%
        1.0M
        SRR27013274_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        28.0%
        41.0%
        235bp
        274bp
        9%
        1.0M
        SRR27013274_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        91.3Kbp
        3.0Mbp
        SRR27013275_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.6%
        100.0%
        485.9Mb
        2.1M
        41.5%
        99.8%
        3.7%
        33.9%
        41.0%
        231bp
        264bp
        9%
        1.1M
        SRR27013275_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        31.4%
        41.0%
        232bp
        274bp
        9%
        1.1M
        SRR27013275_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        117.5Kbp
        3.0Mbp
        SRR27013276_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        347.3Mb
        1.4M
        41.6%
        99.9%
        4.1%
        28.4%
        41.0%
        243bp
        294bp
        9%
        0.7M
        SRR27013276_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        25.3%
        41.0%
        244bp
        301bp
        9%
        0.7M
        SRR27013276_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        68.2Kbp
        4.3Mbp
        SRR27013277_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.1%
        100.0%
        279.4Mb
        1.0M
        40.8%
        100.0%
        3.0%
        22.9%
        40.0%
        278bp
        301bp
        9%
        0.5M
        SRR27013277_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        18.8%
        40.0%
        279bp
        301bp
        9%
        0.5M
        SRR27013277_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        64.8Kbp
        3.1Mbp
        SRR27013278_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        347.9Mb
        1.3M
        41.1%
        99.9%
        3.8%
        28.1%
        41.0%
        263bp
        301bp
        9%
        0.7M
        SRR27013278_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        23.6%
        41.0%
        264bp
        301bp
        9%
        0.7M
        SRR27013278_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        100.6Kbp
        3.1Mbp
        SRR27013279_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.1%
        100.0%
        315.2Mb
        1.1M
        41.3%
        100.0%
        3.4%
        26.4%
        41.0%
        277bp
        301bp
        9%
        0.6M
        SRR27013279_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        20.9%
        41.0%
        278bp
        301bp
        9%
        0.6M
        SRR27013279_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        59.3Kbp
        3.1Mbp
        SRR27013280_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        376.9Mb
        1.4M
        41.4%
        100.0%
        3.4%
        30.3%
        41.0%
        265bp
        301bp
        9%
        0.7M
        SRR27013280_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        25.9%
        41.0%
        266bp
        301bp
        9%
        0.7M
        SRR27013280_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        87.4Kbp
        3.0Mbp
        SRR27013281_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.1%
        100.0%
        253.2Mb
        0.9M
        40.6%
        99.9%
        4.6%
        19.9%
        40.0%
        283bp
        301bp
        9%
        0.4M
        SRR27013281_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        17.1%
        40.0%
        285bp
        301bp
        9%
        0.4M
        SRR27013281_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        47.3Kbp
        3.1Mbp
        SRR27013282_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        356.6Mb
        1.3M
        41.2%
        100.0%
        3.6%
        28.3%
        41.0%
        265bp
        301bp
        9%
        0.7M
        SRR27013282_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        23.8%
        41.0%
        266bp
        301bp
        9%
        0.7M
        SRR27013282_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        90.8Kbp
        3.1Mbp
        SRR27013283_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.6%
        100.0%
        482.9Mb
        2.0M
        41.5%
        99.8%
        3.9%
        34.2%
        41.0%
        237bp
        274bp
        9%
        1.0M
        SRR27013283_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        31.5%
        41.0%
        238bp
        284bp
        9%
        1.0M
        SRR27013283_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        109.6Kbp
        3.0Mbp
        SRR27013284_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        495.9Mb
        2.1M
        41.4%
        99.9%
        4.6%
        34.6%
        41.0%
        239bp
        284bp
        9%
        1.0M
        SRR27013284_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        30.8%
        41.0%
        241bp
        294bp
        9%
        1.0M
        SRR27013284_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        82.9Kbp
        3.1Mbp
        SRR27013285_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.5%
        100.0%
        442.7Mb
        1.9M
        41.5%
        99.8%
        4.4%
        32.6%
        41.0%
        237bp
        274bp
        9%
        0.9M
        SRR27013285_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        28.7%
        41.0%
        239bp
        284bp
        9%
        0.9M
        SRR27013285_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        98.0Kbp
        3.0Mbp
        SRR27013286_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.3%
        100.0%
        433.4Mb
        1.7M
        41.5%
        99.9%
        4.1%
        32.0%
        41.0%
        249bp
        294bp
        9%
        0.9M
        SRR27013286_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        27.5%
        41.0%
        251bp
        301bp
        9%
        0.9M
        SRR27013286_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        96.7Kbp
        3.0Mbp
        SRR27013287_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        317.1Mb
        1.2M
        40.9%
        100.0%
        3.2%
        24.9%
        40.0%
        271bp
        301bp
        9%
        0.6M
        SRR27013287_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        21.1%
        40.0%
        272bp
        301bp
        9%
        0.6M
        SRR27013287_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        108.9Kbp
        3.0Mbp
        SRR27013288_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.1%
        100.0%
        282.9Mb
        1.0M
        40.9%
        100.0%
        3.1%
        23.5%
        40.0%
        273bp
        301bp
        9%
        0.5M
        SRR27013288_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        19.5%
        41.0%
        274bp
        301bp
        9%
        0.5M
        SRR27013288_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        80.0Kbp
        3.0Mbp
        SRR27013289_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.2%
        100.0%
        361.4Mb
        1.4M
        41.3%
        100.0%
        3.5%
        29.4%
        41.0%
        266bp
        301bp
        9%
        0.7M
        SRR27013289_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        24.1%
        41.0%
        267bp
        301bp
        9%
        0.7M
        SRR27013289_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        89.8Kbp
        3.0Mbp
        SRR27013290_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        397.0Mb
        1.6M
        41.4%
        99.9%
        3.6%
        30.7%
        41.0%
        244bp
        294bp
        9%
        0.8M
        SRR27013290_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        27.0%
        41.0%
        246bp
        294bp
        9%
        0.8M
        SRR27013290_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        88.2Kbp
        3.0Mbp
        SRR27013291_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.5%
        100.0%
        463.2Mb
        2.0M
        41.2%
        99.8%
        3.9%
        32.4%
        41.0%
        230bp
        274bp
        9%
        1.0M
        SRR27013291_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        29.2%
        41.0%
        232bp
        274bp
        9%
        1.0M
        SRR27013291_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        163.4Kbp
        3.1Mbp
        SRR27013292_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.1%
        100.0%
        249.1Mb
        0.9M
        40.9%
        99.9%
        5.7%
        21.9%
        40.0%
        284bp
        301bp
        9%
        0.4M
        SRR27013292_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        17.9%
        41.0%
        286bp
        301bp
        9%
        0.4M
        SRR27013292_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        23.5Kbp
        3.0Mbp
        SRR27013293_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        0.4%
        100.0%
        484.6Mb
        2.0M
        41.7%
        99.9%
        3.5%
        33.3%
        41.0%
        244bp
        284bp
        9%
        1.0M
        SRR27013293_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        30.4%
        41.0%
        245bp
        294bp
        9%
        1.0M
        SRR27013293_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        52.4Kbp
        3.9Mbp

        QUAST

        Quality assessment tool for genome assemblies.URL: http://quast.bioinf.spbau.ruDOI: 10.1093/bioinformatics/btt086

        Assembly Statistics

        Showing 49/49 rows and 4/4 columns.
        Sample NameN50 (Kbp)L50 (K)Largest contig (Kbp)Length (Mbp)
        SRR27013147_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        182.2Kbp
        0.0K
        295.2Kbp
        3.1Mbp
        SRR27013245_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        45.1Kbp
        0.1K
        189.6Kbp
        8.4Mbp
        SRR27013246_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        106.6Kbp
        0.0K
        333.7Kbp
        3.0Mbp
        SRR27013247_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        74.6Kbp
        0.0K
        280.7Kbp
        3.1Mbp
        SRR27013248_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        32.7Kbp
        0.0K
        165.6Kbp
        3.0Mbp
        SRR27013249_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        64.3Kbp
        0.0K
        255.6Kbp
        3.0Mbp
        SRR27013250_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        75.0Kbp
        0.0K
        255.6Kbp
        3.0Mbp
        SRR27013251_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        10.8Kbp
        0.1K
        121.8Kbp
        5.3Mbp
        SRR27013253_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        72.4Kbp
        0.0K
        255.6Kbp
        3.1Mbp
        SRR27013254_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        32.0Kbp
        0.0K
        157.2Kbp
        3.0Mbp
        SRR27013255_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        91.3Kbp
        0.0K
        268.5Kbp
        3.0Mbp
        SRR27013256_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        55.1Kbp
        0.0K
        173.3Kbp
        3.1Mbp
        SRR27013257_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        33.1Kbp
        0.0K
        101.0Kbp
        3.0Mbp
        SRR27013258_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        27.6Kbp
        0.0K
        160.5Kbp
        3.0Mbp
        SRR27013259_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        24.4Kbp
        0.0K
        83.3Kbp
        3.1Mbp
        SRR27013260_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        32.0Kbp
        0.0K
        181.6Kbp
        3.0Mbp
        SRR27013261_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        98.0Kbp
        0.0K
        237.1Kbp
        3.0Mbp
        SRR27013262_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        38.9Kbp
        0.0K
        150.0Kbp
        3.1Mbp
        SRR27013263_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        87.5Kbp
        0.0K
        239.9Kbp
        3.0Mbp
        SRR27013264_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        101.4Kbp
        0.0K
        278.3Kbp
        3.0Mbp
        SRR27013265_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        119.8Kbp
        0.0K
        298.0Kbp
        3.0Mbp
        SRR27013266_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        228.4Kbp
        0.0K
        427.7Kbp
        3.0Mbp
        SRR27013267_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        57.3Kbp
        0.0K
        264.9Kbp
        3.0Mbp
        SRR27013268_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        295.2Kbp
        0.0K
        454.9Kbp
        3.0Mbp
        SRR27013269_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        93.3Kbp
        0.0K
        244.6Kbp
        3.0Mbp
        SRR27013270_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        38.0Kbp
        0.0K
        158.3Kbp
        3.0Mbp
        SRR27013271_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        75.8Kbp
        0.0K
        237.1Kbp
        3.0Mbp
        SRR27013272_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        98.7Kbp
        0.0K
        413.0Kbp
        3.1Mbp
        SRR27013273_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        110.6Kbp
        0.0K
        273.0Kbp
        3.0Mbp
        SRR27013274_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        91.3Kbp
        0.0K
        262.3Kbp
        3.0Mbp
        SRR27013275_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        117.5Kbp
        0.0K
        291.5Kbp
        3.0Mbp
        SRR27013276_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        68.2Kbp
        0.0K
        303.4Kbp
        4.3Mbp
        SRR27013277_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        64.8Kbp
        0.0K
        181.5Kbp
        3.1Mbp
        SRR27013278_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        100.6Kbp
        0.0K
        291.5Kbp
        3.1Mbp
        SRR27013279_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        59.3Kbp
        0.0K
        214.1Kbp
        3.1Mbp
        SRR27013280_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        87.4Kbp
        0.0K
        237.1Kbp
        3.0Mbp
        SRR27013281_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        47.3Kbp
        0.0K
        181.5Kbp
        3.1Mbp
        SRR27013282_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        90.8Kbp
        0.0K
        255.5Kbp
        3.1Mbp
        SRR27013283_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        109.6Kbp
        0.0K
        270.3Kbp
        3.0Mbp
        SRR27013284_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        82.9Kbp
        0.0K
        244.4Kbp
        3.1Mbp
        SRR27013285_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        98.0Kbp
        0.0K
        335.5Kbp
        3.0Mbp
        SRR27013286_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        96.7Kbp
        0.0K
        266.8Kbp
        3.0Mbp
        SRR27013287_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        108.9Kbp
        0.0K
        183.9Kbp
        3.0Mbp
        SRR27013288_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        80.0Kbp
        0.0K
        197.1Kbp
        3.0Mbp
        SRR27013289_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        89.8Kbp
        0.0K
        249.0Kbp
        3.0Mbp
        SRR27013290_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        88.2Kbp
        0.0K
        280.2Kbp
        3.0Mbp
        SRR27013291_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        163.4Kbp
        0.0K
        377.6Kbp
        3.1Mbp
        SRR27013292_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        23.5Kbp
        0.0K
        71.5Kbp
        3.0Mbp
        SRR27013293_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_contigs
        52.4Kbp
        0.0K
        255.6Kbp
        3.9Mbp

        Number of Contigs

        This plot shows the number of contigs found for each assembly, broken down by length.

        Created with MultiQC

        fastp

        Version: 0.23.2

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC


        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        100 samples had less than 1% of reads made up of overrepresented sequences

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 2/2 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
        40
        56381
        0.0794%
        AACTAAAACCGATCCATCATCAAAAACAGAAATTTGAACAGGTTGATAAT
        2
        1173
        0.0017%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1
        fastp0.23.2